South African citizens are visa nationals, they require a visa to travel to the UK.
Being resident in Portugal does not make them "EU citizens". An EU citizen is someone who holds a passport issued by an EU country, not just a residence permit.
The ETA UK scheme will only apply for people who are non-visa nationals, i.e. people who do not need a visa anyway. It is not a visa or eVisa, it will only be a prerequisite to being able to travel to the UK for people who are already allowed to enter the UK without a visa.
Where they should apply from will depend on when they intend to travel, though it can be tricky to apply with a limited history in their current place of residence (as they will have to provide evidence of their situation and financials for several months in their application). It also depends on their current situation in South Africa (i.e. current stable, well paid job, for instance).